From d184380bc0cf49fe534b94d0a657e29c9931b557 Mon Sep 17 00:00:00 2001
From: Stephan Schiffels <schiffels_schiffels@mac.com>
Date: Tue, 18 Sep 2018 17:25:10 +0200
Subject: [PATCH] fixed stupid bug that would cause range errors in the -I
 option when using a list of indices other than 0,1,2,3...

---
 msmc2.d | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/msmc2.d b/msmc2.d
index ae58aee..73f2d5b 100644
--- a/msmc2.d
+++ b/msmc2.d
@@ -135,9 +135,9 @@ void parseCommandLine(string[] args) {
   void handleIndices(string option, string value) {
     try {
       auto hapIndices = std.string.split(value, ",").map!"a.to!size_t()"().array();
-      foreach(i; hapIndices[0..$-1])
-        foreach(j; hapIndices[i..$])
-          pairIndices ~= [i, j];
+      foreach(i; 0..(hapIndices.length - 1))
+        foreach(j; (i + 1)..hapIndices.length)
+          pairIndices ~= [hapIndices[i], hapIndices[j]];
     }
     catch(ConvException e) {
       auto pairIndexSubStrings = std.string.split(value, ",");